qiime2lefse

[Ravibiokr]

Dear LefSe,

i have tried to formate qiime produced otu biom file to use in lefse by using qiime2lefse.py

i got error as follows in qiime-1.8 VM mechine

python qiime2lefse.py --in 1_8_otu_table_chimera_filtered_w_tax.biom --md 1_8_otu_table_chimera_filtered.biom --out qiimetolefse
Traceback (most recent call last):
  File "qiime2lefse.py", line 85, in <module>
    sel_md  = [pars['c'],pars['s'],pars['u']])
  File "qiime2lefse.py", line 45, in qiime2lefse
    for i,(l1,l2) in enumerate(zip( lines[0], lines[-1] )):
IndexError: list index out of range


How to use qiime data in lefse?

Thank you

Ravi

[Nicola Segata]

Hi Ravi,

 thanks to George Weingart, we just uploaded a new version of LEfSe which accepts natively the biom format. So you can now use it directly without relying on qiime2lefse.py.

many thanks

Nicola

[Joe Moore]

Hi Nicola,

I uploaded my QIIME-generated biom file onto the Galaxy site, but LEfSe didn't recognize it when I tried to proceed to formatting. What processing do I need to do to the QIIME biom file beforehand?

Thanks! 

Joe

[George Weingart]

Hi Joe,

We implemented the option to import biom files into lefse in the batch mode,  not yet in Galaxy.

So please try it in batch and let me know if you encounter problems.

If there will be demand to use that option in Galaxy, I'll suggest we implement it in Galaxy as well.

Best regards,

George 

[sampie]

Hi George,

I am wondering how importing biom files to lefse exactly works. I have an otu_table.biom generated by Qiime. The sample metadata has been added to the biom file with "biom add-metadata -i otu_table.biom -o otu_table_md.biom -m 130037-metadata.txt". The sample metadata has a group named "Group". Each sample is assigned into one of the following group values: "Cellu", "Pexy" or "Norm".

Running command gives error messages:
"format_input.py otu_table_md.biom otu_table_md.lefse -biom_c Group -c 1 -o 1000000"

Traceback (most recent call last):

  File "/home/apps/lefse/format_input.py", line 433, in <module>
    feats = numerical_values(feats,params['norm_v'])
  File "/home/apps/lefse/format_input.py", line 174, in numerical_values
    feats[k] = [float(val) for val in v]
ValueError: could not convert string to float: Cellu

What exact steps/commands are needed in order to run lefse analysis for a biom file?

BR
Sami